1 The impatient can try:
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8 Clustal-Omega needs argtable2 (http://argtable.sourceforge.net/). If
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9 argtable2 is installed in a non-standard directory you might have to
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10 point configure to its installation directory. For example, if you are
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11 on a Mac and have argtable installed via MacPorts then you should use
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12 the following command line:
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14 $ ./configure CFLAGS='-I/opt/local/include' LDFLAGS='-L/opt/local/lib'
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16 ClustalO will automatically support multi-threading if your compiler
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17 supports OpenMP. For some reason automake's OpenMP detection for
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18 Apple's gcc is broken. You can force OpenMP detection by calling configure
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21 $ ./configure OPENMP_CFLAGS='-fopenmp' CFLAGS='-DHAVE_OPENMP'
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23 You could use a non-Apple gcc installed via MacPorts, adding
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25 CC=/opt/local/bin/gcc-mp-4.5
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27 to the configure call (you will have to change the exact string to match
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30 See below for generic installation instructions:
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32 ----------------------------------------------------------------------
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36 Installation Instructions
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37 *************************
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39 Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005,
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40 2006, 2007, 2008, 2009 Free Software Foundation, Inc.
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42 Copying and distribution of this file, with or without modification,
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43 are permitted in any medium without royalty provided the copyright
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44 notice and this notice are preserved. This file is offered as-is,
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45 without warranty of any kind.
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50 Briefly, the shell commands `./configure; make; make install' should
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51 configure, build, and install this package. The following
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52 more-detailed instructions are generic; see the `README' file for
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53 instructions specific to this package. Some packages provide this
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54 `INSTALL' file but do not implement all of the features documented
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55 below. The lack of an optional feature in a given package is not
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56 necessarily a bug. More recommendations for GNU packages can be found
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57 in *note Makefile Conventions: (standards)Makefile Conventions.
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59 The `configure' shell script attempts to guess correct values for
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60 various system-dependent variables used during compilation. It uses
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61 those values to create a `Makefile' in each directory of the package.
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62 It may also create one or more `.h' files containing system-dependent
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63 definitions. Finally, it creates a shell script `config.status' that
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64 you can run in the future to recreate the current configuration, and a
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65 file `config.log' containing compiler output (useful mainly for
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66 debugging `configure').
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68 It can also use an optional file (typically called `config.cache'
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69 and enabled with `--cache-file=config.cache' or simply `-C') that saves
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70 the results of its tests to speed up reconfiguring. Caching is
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71 disabled by default to prevent problems with accidental use of stale
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74 If you need to do unusual things to compile the package, please try
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75 to figure out how `configure' could check whether to do them, and mail
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76 diffs or instructions to the address given in the `README' so they can
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77 be considered for the next release. If you are using the cache, and at
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78 some point `config.cache' contains results you don't want to keep, you
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79 may remove or edit it.
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81 The file `configure.ac' (or `configure.in') is used to create
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82 `configure' by a program called `autoconf'. You need `configure.ac' if
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83 you want to change it or regenerate `configure' using a newer version
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86 The simplest way to compile this package is:
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88 1. `cd' to the directory containing the package's source code and type
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89 `./configure' to configure the package for your system.
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91 Running `configure' might take a while. While running, it prints
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92 some messages telling which features it is checking for.
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94 2. Type `make' to compile the package.
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96 3. Optionally, type `make check' to run any self-tests that come with
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97 the package, generally using the just-built uninstalled binaries.
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99 4. Type `make install' to install the programs and any data files and
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100 documentation. When installing into a prefix owned by root, it is
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101 recommended that the package be configured and built as a regular
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102 user, and only the `make install' phase executed with root
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105 5. Optionally, type `make installcheck' to repeat any self-tests, but
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106 this time using the binaries in their final installed location.
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107 This target does not install anything. Running this target as a
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108 regular user, particularly if the prior `make install' required
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109 root privileges, verifies that the installation completed
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112 6. You can remove the program binaries and object files from the
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113 source code directory by typing `make clean'. To also remove the
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114 files that `configure' created (so you can compile the package for
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115 a different kind of computer), type `make distclean'. There is
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116 also a `make maintainer-clean' target, but that is intended mainly
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117 for the package's developers. If you use it, you may have to get
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118 all sorts of other programs in order to regenerate files that came
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119 with the distribution.
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121 7. Often, you can also type `make uninstall' to remove the installed
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122 files again. In practice, not all packages have tested that
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123 uninstallation works correctly, even though it is required by the
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124 GNU Coding Standards.
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126 8. Some packages, particularly those that use Automake, provide `make
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127 distcheck', which can by used by developers to test that all other
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128 targets like `make install' and `make uninstall' work correctly.
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129 This target is generally not run by end users.
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131 Compilers and Options
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132 =====================
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134 Some systems require unusual options for compilation or linking that
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135 the `configure' script does not know about. Run `./configure --help'
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136 for details on some of the pertinent environment variables.
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138 You can give `configure' initial values for configuration parameters
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139 by setting variables in the command line or in the environment. Here
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142 ./configure CC=c99 CFLAGS=-g LIBS=-lposix
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144 *Note Defining Variables::, for more details.
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146 Compiling For Multiple Architectures
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147 ====================================
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149 You can compile the package for more than one kind of computer at the
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150 same time, by placing the object files for each architecture in their
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151 own directory. To do this, you can use GNU `make'. `cd' to the
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152 directory where you want the object files and executables to go and run
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153 the `configure' script. `configure' automatically checks for the
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154 source code in the directory that `configure' is in and in `..'. This
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155 is known as a "VPATH" build.
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157 With a non-GNU `make', it is safer to compile the package for one
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158 architecture at a time in the source code directory. After you have
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159 installed the package for one architecture, use `make distclean' before
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160 reconfiguring for another architecture.
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162 On MacOS X 10.5 and later systems, you can create libraries and
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163 executables that work on multiple system types--known as "fat" or
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164 "universal" binaries--by specifying multiple `-arch' options to the
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165 compiler but only a single `-arch' option to the preprocessor. Like
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168 ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
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169 CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
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170 CPP="gcc -E" CXXCPP="g++ -E"
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172 This is not guaranteed to produce working output in all cases, you
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173 may have to build one architecture at a time and combine the results
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174 using the `lipo' tool if you have problems.
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179 By default, `make install' installs the package's commands under
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180 `/usr/local/bin', include files under `/usr/local/include', etc. You
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181 can specify an installation prefix other than `/usr/local' by giving
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182 `configure' the option `--prefix=PREFIX', where PREFIX must be an
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183 absolute file name.
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185 You can specify separate installation prefixes for
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186 architecture-specific files and architecture-independent files. If you
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187 pass the option `--exec-prefix=PREFIX' to `configure', the package uses
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188 PREFIX as the prefix for installing programs and libraries.
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189 Documentation and other data files still use the regular prefix.
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191 In addition, if you use an unusual directory layout you can give
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192 options like `--bindir=DIR' to specify different values for particular
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193 kinds of files. Run `configure --help' for a list of the directories
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194 you can set and what kinds of files go in them. In general, the
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195 default for these options is expressed in terms of `${prefix}', so that
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196 specifying just `--prefix' will affect all of the other directory
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197 specifications that were not explicitly provided.
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199 The most portable way to affect installation locations is to pass the
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200 correct locations to `configure'; however, many packages provide one or
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201 both of the following shortcuts of passing variable assignments to the
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202 `make install' command line to change installation locations without
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203 having to reconfigure or recompile.
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205 The first method involves providing an override variable for each
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206 affected directory. For example, `make install
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207 prefix=/alternate/directory' will choose an alternate location for all
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208 directory configuration variables that were expressed in terms of
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209 `${prefix}'. Any directories that were specified during `configure',
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210 but not in terms of `${prefix}', must each be overridden at install
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211 time for the entire installation to be relocated. The approach of
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212 makefile variable overrides for each directory variable is required by
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213 the GNU Coding Standards, and ideally causes no recompilation.
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214 However, some platforms have known limitations with the semantics of
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215 shared libraries that end up requiring recompilation when using this
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216 method, particularly noticeable in packages that use GNU Libtool.
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218 The second method involves providing the `DESTDIR' variable. For
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219 example, `make install DESTDIR=/alternate/directory' will prepend
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220 `/alternate/directory' before all installation names. The approach of
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221 `DESTDIR' overrides is not required by the GNU Coding Standards, and
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222 does not work on platforms that have drive letters. On the other hand,
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223 it does better at avoiding recompilation issues, and works well even
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224 when some directory options were not specified in terms of `${prefix}'
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225 at `configure' time.
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230 If the package supports it, you can cause programs to be installed
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231 with an extra prefix or suffix on their names by giving `configure' the
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232 option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
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234 Some packages pay attention to `--enable-FEATURE' options to
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235 `configure', where FEATURE indicates an optional part of the package.
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236 They may also pay attention to `--with-PACKAGE' options, where PACKAGE
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237 is something like `gnu-as' or `x' (for the X Window System). The
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238 `README' should mention any `--enable-' and `--with-' options that the
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239 package recognizes.
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241 For packages that use the X Window System, `configure' can usually
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242 find the X include and library files automatically, but if it doesn't,
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243 you can use the `configure' options `--x-includes=DIR' and
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244 `--x-libraries=DIR' to specify their locations.
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246 Some packages offer the ability to configure how verbose the
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247 execution of `make' will be. For these packages, running `./configure
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248 --enable-silent-rules' sets the default to minimal output, which can be
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249 overridden with `make V=1'; while running `./configure
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250 --disable-silent-rules' sets the default to verbose, which can be
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251 overridden with `make V=0'.
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256 On HP-UX, the default C compiler is not ANSI C compatible. If GNU
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257 CC is not installed, it is recommended to use the following options in
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258 order to use an ANSI C compiler:
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260 ./configure CC="cc -Ae -D_XOPEN_SOURCE=500"
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262 and if that doesn't work, install pre-built binaries of GCC for HP-UX.
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264 On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot
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265 parse its `<wchar.h>' header file. The option `-nodtk' can be used as
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266 a workaround. If GNU CC is not installed, it is therefore recommended
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269 ./configure CC="cc"
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271 and if that doesn't work, try
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273 ./configure CC="cc -nodtk"
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275 On Solaris, don't put `/usr/ucb' early in your `PATH'. This
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276 directory contains several dysfunctional programs; working variants of
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277 these programs are available in `/usr/bin'. So, if you need `/usr/ucb'
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278 in your `PATH', put it _after_ `/usr/bin'.
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280 On Haiku, software installed for all users goes in `/boot/common',
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281 not `/usr/local'. It is recommended to use the following options:
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283 ./configure --prefix=/boot/common
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285 Specifying the System Type
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286 ==========================
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288 There may be some features `configure' cannot figure out
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289 automatically, but needs to determine by the type of machine the package
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290 will run on. Usually, assuming the package is built to be run on the
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291 _same_ architectures, `configure' can figure that out, but if it prints
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292 a message saying it cannot guess the machine type, give it the
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293 `--build=TYPE' option. TYPE can either be a short name for the system
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294 type, such as `sun4', or a canonical name which has the form:
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298 where SYSTEM can have one of these forms:
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303 See the file `config.sub' for the possible values of each field. If
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304 `config.sub' isn't included in this package, then this package doesn't
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305 need to know the machine type.
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307 If you are _building_ compiler tools for cross-compiling, you should
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308 use the option `--target=TYPE' to select the type of system they will
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311 If you want to _use_ a cross compiler, that generates code for a
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312 platform different from the build platform, you should specify the
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313 "host" platform (i.e., that on which the generated programs will
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314 eventually be run) with `--host=TYPE'.
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319 If you want to set default values for `configure' scripts to share,
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320 you can create a site shell script called `config.site' that gives
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321 default values for variables like `CC', `cache_file', and `prefix'.
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322 `configure' looks for `PREFIX/share/config.site' if it exists, then
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323 `PREFIX/etc/config.site' if it exists. Or, you can set the
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324 `CONFIG_SITE' environment variable to the location of the site script.
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325 A warning: not all `configure' scripts look for a site script.
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330 Variables not defined in a site shell script can be set in the
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331 environment passed to `configure'. However, some packages may run
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332 configure again during the build, and the customized values of these
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333 variables may be lost. In order to avoid this problem, you should set
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334 them in the `configure' command line, using `VAR=value'. For example:
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336 ./configure CC=/usr/local2/bin/gcc
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338 causes the specified `gcc' to be used as the C compiler (unless it is
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339 overridden in the site shell script).
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341 Unfortunately, this technique does not work for `CONFIG_SHELL' due to
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342 an Autoconf bug. Until the bug is fixed you can use this workaround:
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344 CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash
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346 `configure' Invocation
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347 ======================
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349 `configure' recognizes the following options to control how it
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354 Print a summary of all of the options to `configure', and exit.
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358 Print a summary of the options unique to this package's
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359 `configure', and exit. The `short' variant lists options used
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360 only in the top level, while the `recursive' variant lists options
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361 also present in any nested packages.
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365 Print the version of Autoconf used to generate the `configure'
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368 `--cache-file=FILE'
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369 Enable the cache: use and save the results of the tests in FILE,
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370 traditionally `config.cache'. FILE defaults to `/dev/null' to
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375 Alias for `--cache-file=config.cache'.
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380 Do not print messages saying which checks are being made. To
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381 suppress all normal output, redirect it to `/dev/null' (any error
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382 messages will still be shown).
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385 Look for the package's source code in directory DIR. Usually
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386 `configure' can determine that directory automatically.
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389 Use DIR as the installation prefix. *note Installation Names::
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390 for more details, including other options available for fine-tuning
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391 the installation locations.
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395 Run the configure checks, but stop before creating any output
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398 `configure' also accepts some other, not widely useful, options. Run
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399 `configure --help' for more details.
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